Variant report

Variant	rs2753403
Chromosome Location	chr14:68913185-68913186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68887949..68890328-chr14:68911065..68913436,2	MCF-7	breast:
2	chr14:68848862..68851704-chr14:68911488..68914021,2	MCF-7	breast:
3	chr14:68911957..68914084-chr14:69032259..69034812,2	MCF-7	breast:
4	chr14:68771399..68773960-chr14:68910018..68913627,3	MCF-7	breast:
5	chr14:68912559..68915110-chr14:68915133..68917933,3	MCF-7	breast:
6	chr14:68911921..68914411-chr14:69260879..69263149,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction
ENSG00000258477	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10454686	0.85[CEU][hapmap]
rs10747299	0.85[ASN][1000 genomes]
rs11158737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11158742	1.00[JPT][hapmap]
rs11845050	0.85[LWK][hapmap]
rs12435006	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12588330	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12889206	0.86[MEX][hapmap]
rs12897307	1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17755674	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1956538	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2064910	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2331703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525507	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842320	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784118	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3966077	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4899241	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4899243	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4902571	0.90[CEU][hapmap];0.86[MEX][hapmap]
rs4902578	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4902580	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4902581	1.00[JPT][hapmap]
rs4902582	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573834	0.86[MEX][hapmap]
rs66597987	0.80[EUR][1000 genomes]
rs7140827	0.82[EUR][1000 genomes]
rs7145422	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7150454	0.86[MEX][hapmap]
rs8003606	1.00[CHB][hapmap]
rs8009876	0.86[MEX][hapmap]
rs8013026	0.85[CEU][hapmap]
rs8015516	0.90[CEU][hapmap]
rs8019592	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9323510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9743896	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975422	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2753403	C14orf50	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68895200-68914400	Weak transcription	A549	lung
2	chr14:68906800-68916000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr14:68908600-68917400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr14:68909000-68916200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr14:68909600-68915000	Enhancers	Dnd41	blood
6	chr14:68911400-68915000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr14:68911600-68913400	Weak transcription	Placenta	Placenta
8	chr14:68911600-68914800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:68911600-68914800	Weak transcription	Small Intestine	intestine
10	chr14:68911800-68913600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:68911800-68914000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr14:68911800-68916200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr14:68911800-68916200	Weak transcription	Brain Anterior Caudate	brain
14	chr14:68911800-68916200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr14:68911800-68916200	Weak transcription	NH-A	brain
16	chr14:68911800-68917200	Weak transcription	Right Atrium	heart
17	chr14:68911800-68917600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:68911800-68921200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:68912000-68913400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr14:68912000-68913600	Weak transcription	Liver	Liver
21	chr14:68912000-68913800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr14:68912000-68914400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr14:68912000-68914400	Weak transcription	Fetal Stomach	stomach
24	chr14:68912000-68914600	Weak transcription	Fetal Muscle Leg	muscle
25	chr14:68912000-68914800	Weak transcription	Stomach Mucosa	stomach
26	chr14:68912000-68914800	Weak transcription	NHLF	lung
27	chr14:68912000-68915000	Weak transcription	Pancreas	Pancrea
28	chr14:68912000-68916000	Weak transcription	Fetal Thymus	thymus
29	chr14:68912000-68916000	Weak transcription	NHDF-Ad	bronchial
30	chr14:68912000-68916200	Weak transcription	Brain Hippocampus Middle	brain
31	chr14:68912000-68916200	Weak transcription	Ovary	ovary
32	chr14:68912000-68916200	Weak transcription	HMEC	breast
33	chr14:68912000-68916800	Weak transcription	Brain Germinal Matrix	brain
34	chr14:68912000-68917600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:68912000-68917600	Weak transcription	Left Ventricle	heart
36	chr14:68912000-68917600	Weak transcription	Psoas Muscle	Psoas
37	chr14:68912200-68914600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr14:68912200-68914600	Weak transcription	Fetal Lung	lung
39	chr14:68912200-68915400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr14:68912200-68916000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr14:68912200-68916000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:68912200-68916200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr14:68912200-68916200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr14:68912200-68916200	Weak transcription	Adipose Nuclei	Adipose
45	chr14:68912200-68916600	Weak transcription	HSMMtube	muscle
46	chr14:68912200-68917200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr14:68912200-68917600	Weak transcription	Osteobl	bone
48	chr14:68912400-68916000	Weak transcription	HSMM	muscle
49	chr14:68912600-68913800	Enhancers	Colon Smooth Muscle	Colon
50	chr14:68912600-68914000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links